Dear Colleagues,
We are delighted to announce the 2nd edition of the crystallographic school in
Thailand, SEA COAST - SouthEast Asian Crystallographic Overview And Systematic
Training.
The workshop will take place on January 21 - 29, 2020, at the King Mongkut's
University of Technology Thonburi
Hi Anirban,
It would be great if you could share the compilation of relevant responses to
your request. I think many others in the community could use these examples for
educational purposes.
Best,
Nukri
Ruslan Sanishvili (Nukri), Ph.D.
Macromolecular Crystallographer
GM/CA@APS
X-ray
Hi Bernhard,
While I do not disagree with anything you have said, there is an error in your
computation. Your results are based on the assumption of a 40-hour work week
and one-month vacation in a year.
I don't know about now but back then Russian scientists did not work like that.
So, the
Hi Annette,
I do not have any experience with the particular set up you are using, but just
from general considerations, how about:
1. If you have control over humidity in the room, reduce it as much as you
can during "icy" data collections
2. In another e-mail you mentioned you use
Hi Chenjun Tang,
I have not followed the original discussion, so my apologies if I am repeating
the device already given to you.
Crystallization optimization is always a good idea - nothing beats good quality
crystals. In addition,
you should try collecting few images, especially in the
Difficult to guess from what is visible of the protein but is this density on a
two-fold axis?
Or, it could be Slimer the ghost...
Cheers,
Nukri
Ruslan Sanishvili (Nukri), Ph.D.
Macromolecular Crystallographer
GM/CA@APS
X-ray Science Division, ANL
9700 S. Cass Ave.
Lemont, IL 60439
Tel:
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Sanishvili,
Ruslan [rsanishv...@anl.gov]
Sent: Monday, March 27, 2017 3:09 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] REMINDER: 10th CCP4/APS Crystallographic School in the USA
Dear Colleagues
, ANL
9700 S. Cass Ave.
Lemont, IL 60439
Tel: (630)252-0665
Fax: (630)252-0667
rsanishv...@anl.gov
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Sanishvili,
Ruslan [rsanishv...@anl.gov]
Sent: Wednesday, February 01, 2017 2:51 PM
To: CCP4BB
Dear Colleagues,
We are pleased to announce the 10th annual CCP4 crystallographic school “>From
data collection to structure refinement and beyond”, held at Advanced Photon
Source (APS), Argonne National Laboratory (ANL). All details can be found at
Perfect segue to bring us back to the origin of this thread. Graeme was
reminding the users of Xia2 that Xia2 was using other software for data
analysis and that other software to be credited as well. Indeed, when we
extract "Xia2 has been used for PDB files reported in X high-impact
-0667
rsanishv...@anl.gov
From: Sanishvili, Ruslan
Sent: Wednesday, January 07, 2015 2:22 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Announcement: CCP4 crystallographic summer school in USA, at APS, June
16-23
Dear Colleagues,
We are pleased to announce the eighth annual
Dear Colleagues,
We are pleased to announce the eighth annual CCP4 crystallographic summer
school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All
details can be found at
http://www.ccp4.ac.uk/schools/APS-2015/index.phphttp://www.ccp4.ac.uk/schools/APS-2014/index.php
Dear Graeme,
Could you elaborate on There are also some subtleties to making (b) work
properly... some more? I have a feeling, from observing the beamline users,
that many choose to use this option. It would be very helpful for them to know
what are those subtleties and how to best make it
Hi Jacob,
I'll take a first crack as I am sure many will follow.
It is true that with CCD detectors one has to be careful how small an
oscillation range to use for a frame before read noise starts to eat into the
data quality.
Pilatus offers two major new features - is fast and is photon
:33 AM
To: Sanishvili, Ruslan
Cc: ccp4bb@jiscmail.ac.uk
Subject: Re: [ccp4bb] metals disapear
If metal ion will be sensitive to radiation depends on its redox chemistry
and not its X-ray properties. For a metal to be affected by radiation dose
it needs to be reduced by free radicals. However
@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Reply-To: Sanishvili, Ruslan rsanishv...@anl.govmailto:rsanishv...@anl.gov
Dear Colleagues,
We are pleased to announce the seventh annual CCP4 crystallographic summer
school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All
details can
Ruslan Sanishvili (Nukri)
Macromolecular Crystallographer
GM/CA@APS
X-ray Science Division, ANL
9700 S. Cass Ave.
Lemont, IL 60439
Tel: (630)252-0665
Fax: (630)252-0667
rsanishv...@anl.gov
From: Sanishvili, Ruslan rsanishv...@anl.govmailto:rsanishv...@anl.gov
Subject: [ccp4bb] CCP4
Dear Colleagues,
We are pleased to announce the seventh annual CCP4 crystallographic summer
school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All
details can be found at
http://www.ccp4.ac.uk/schools/APS-2014/index.php
Title:CCP4 crystallographic school: From data
Hi Rhis,
It may have been suggested already but still...
X-ray fluorescence spectra can often tell you what elements you may be dealing
with. Spectra won't tell anything about binding specifics, but any extra bit of
information could help. Any descent synchrotron MX beamline, equipped for
Hi Uma,
I wish you would have shown negative densities on Fo-Fc maps as well.
You protein (and the template one) may end up being a classical case to
demonstrate how radiation-induced changes may lead to undesirable
interpretations. Especially because it is a Cys and because it is in the active
From: Sanishvili, Ruslan
Sent: Tuesday, April 03, 2012 5:15 PM
To: CCP4BB@JISCMAIL.AC.UK
Cc: Sanishvili, Ruslan
Subject: Application deadline approaching: CCP4 summer school at APS, in USA
Dear Colleagues,
We would like to point out that the application deadline for the 5th annual
Hi Chris,
As has been suggested already, and seems quite plausible to me, it sounds like
tell-tale signs of radiation damage.
To have little more substance behind this suspicion, some more experimental
details could help:
What was the dose accumulated during data collection?
If the dose cannot
Dear Colleagues,
We would like to point out that the application deadline for the 5th annual
CCP4 Summer School From data collection to structure refinement and beyond is
April 17, 2012. The school will take place from June 19 through June 26, 2012
at the Advanced Photon Source (APS) near
: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Sanishvili, Ruslan
Sent: Monday, December 19, 2011 11:37 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Annual CCP4 summer school in USA, at APS, June 19-26
Dear Colleagues,
We are pleased to announce the fifth annual CCP4 summer
Hi Harry,
Are you advertising our CCP4 Summer School coming up in June at APS?
If not, then I'll shamelessly plug in: http://www.ccp4.ac.uk/schools/APS-school/
And if one visits previous years' school links, there are plenty of lectures
posted.
Thanks,
N.
Ruslan Sanishvili (Nukri), Ph.D.
Dear Colleagues,
We are pleased to announce the fifth annual CCP4 summer school at Advanced
Photon Source (APS), Argonne National Laboratory (ANL). All details can be
found at http://www.ccp4.ac.uk/schools/APS-2012/
Title:
CCP4 school: From data collection to structure refinement and beyond
in occasional bubbling.
Ruslan Sanishvili (Nukri), Ph.D.
GM/CA-CAT
Biosciences Division, ANL
9700 S. Cass Ave.
Argonne, IL 60439
Tel: (630)252-0665
Fax: (630)252-0667
rsanishv...@anl.gov
On 11/20/2011 5:22 PM, Sanishvili, Ruslan wrote:
Hi James,
I don't think the comment you referenced meant to imply
Hi James,
I don't think the comment you referenced meant to imply dark progression of
radiation damage. If I remember from the recent thread, it was to say that if
you can only collect few (3?) shots from one crystal before it's too dead and
you use 1st of these shots to devise the strategy,
In fact, just estimating ORGX and ORGY from the first frame, using adxv or
XDS-viewer, seems to do a good job.
The silver lining of having ice (or any other kind) rings is that one can
determine the origin rather accurately by just finding the center of these
rings.
Cheers,
N.
Ruslan
Hi James,
Not as many responses on lysozyme crystallization as I would have expected. Or
may be people thought you were joking (were you?).
Anyhow, higher concentrations of lyso gives smaller crystals but if you let
them grow on their own, you may get few huge ones instead. What worked for me
The milk solution is a suspension of lots of micro-crystals which form
when temperature goes down. When you take the solution out, it worms up
and the crystals dissolve. If you take a look at them under high
magnification microscope in the cold room, chances are you'll see those
crystals. I cannot
Hi dengzq1987,
You don't say how many axes are long. I will assume one. In that case, here is
a compilation of what others have already recommended, with some additions:
1. Orient the crystal so that the long axis is along the rotation axis. It can
be done during mounting the crystal on the
Pictures are helpful to narrow the range of recommendations. It would be even
more helpful to see the entire image, to know the orientation of the rotation
axis, detector distance used, frame width, and any other information on the
setup you can provide.
Nukri
Ruslan Sanishvili (Nukri),
Hi All,
Notwithstanding the stimulating discussion about the B-factor, I'd like
to chime in with my $0.02 on the original question of to build or not to
build and what are the rules and standards... and sorry for the lengthy
e-mail - I was trying to respond to several comments at once.
I thought
Dear Colleagues,
This is a reminder that the deadline for applications for the 4th annual
CCP4 summer school From data collection to structure refinement and
beyond is April 8. The school will take place June 7-15, 2011 at the
Advanced Photon Source (APS) near Chicago.
There is no
Hi Sadaf,
Most likely you are dealing with radiation damage. If that's the case, you
would need to refine occupancies as Mario has already suggested. However, you
may not find a double conformation. Instead, you may find that some of your
sulfurs are gone.
There is a ton of publications on
Dear Colleagues,
This is a reminder that the on-line applications are being accepted for
the 4th annual CCP4 summer school From data collection to structure
refinement and beyond, which will take place early June, 2011 at the
APS near Chicago.
There is no registration fee for the school.
Dear Colleagues,
Building on the success of the past 3 years, we are pleased to announce
the fourth annual CCP4 summer school at Advanced Photon Source (APS),
Argonne National Laboratory (ANL). All details can be found at
http://www.ccp4.ac.uk/schools/APS-2011/index.php
Title:
CCP4
C'mon now! Everybody knows that frogs in real space become handsome
princes in the reciprocal one...
N.
Ruslan Sanishvili (Nukri), Ph.D.
GM/CA-CAT
Biosciences Division, ANL
9700 S. Cass Ave.
Argonne, IL 60439
Tel: (630)252-0665
Fax: (630)252-0667
rsanishv...@anl.gov
Hi,
What is the pI of your protein? If it happens to be anywhere near your
buffer pH, then you should move away from it.
Have you measured the size of you micro-crystals? You may be surprised
what micro-diffraction can do for you these days.
Good luck!
Nukri
Ruslan Sanishvili (Nukri),
Hi James,
Can you, or anybody else, point me to a publication where ...not that
uncommon for one or more crystal symmetry operators to collapse upon
cryo-cooling...
Thanks,
Nukri
Ruslan Sanishvili (Nukri), Ph.D.
GM/CA-CAT
Biosciences Division, ANL
9700 S. Cass Ave.
Argonne, IL 60439
Tel:
of Sanishvili, Ruslan
Sent: Thu 30/09/2010 15:03
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] difficult P1 crystal
Hi James,
Can you, or anybody else, point me to a publication where ...not that
uncommon for one or more crystal symmetry operators to collapse upon
cryo-cooling...
Thanks,
Nukri
sites are one of the first ones to suffer from radiation damage. And aren't the
functional interpretations the ultimate goal of protein structures?
Cheers,
N.
From: Pavel Afonine [mailto:pafon...@lbl.gov]
Sent: Wed 9/15/2010 5:56 PM
To: Sanishvili, Ruslan
Cc
Hi All,
I have not read all messages in the trace so my apologies if somebody
already pointed out what I have to say.
There is lot of talk about how this or that software treats the riding
hydrogens. What to do with the fact that however these hydrogens are
treated in calculations, they are, in
Dear Colleagues,
This is a third and final call for applications for the third annual
CCP4 school: From data collection to structure refinement and beyond
which will be held at Advanced Photon Source, USA.
Application deadline has been extended from Friday, April 9 to Tuesday,
April 12.
rsanishv...@anl.gov
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Sanishvili, Ruslan
Sent: Wednesday, February 24, 2010 9:38 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Third CCP4 workshop in USA, at APS, June 10-17
Dear Colleagues
Hi Todd,
There are many compounds that have color centers which change color as
soon as they are exposed to X-rays. Some turn, blue, some pink, some
yellow etc. I'm not sure which one is the chameleon in your buffer but
you can bring them separately next time and we can shoot them one by
one.
Dear Colleagues,
Building on the success of the past 2 years, we are pleased to announce
the third annual CCP4 workshop at Advanced Photon Source (APS), Argonne
National Laboratory (ANL). All details can be found at
http://www.ccp4.ac.uk/schools/APS-2010/
Title:
CCP4 school: From data
Best story I've heard on scamming the scammers appeared on BBC some
years ago. Fortunately, it was easy to find it. Take a look at
http://news.bbc.co.uk/2/hi/africa/3887493.stm
Enjoy,
Nukri
Ruslan Sanishvili (Nukri), Ph.D.
GM/CA-CAT
Biosciences Division, ANL
9700 S. Cass Ave.
Argonne, IL 60439
I am not sure if this is exactly what you are asking about but 1nig in
pdb sounds awfully like what you are describing.
Also take a look at J Struct Funct Genomics.
javascript:AL_get(this,%20'jour',%20'J%20Struct%20Funct%20Genomics.');
2004;5(4):231-40 for more detailed description of the
My 2 cents:
Cent #1 But they are slightly different ( may be 50 ev) in different
papers. This statement itself contains the answer - always scan, but it
was already suggested by many. I'd like to get to slightly different
issue here. No oxidation or any other interaction in protein crystals
Hi Richard,
Interesting topic raise you did...
On a philosophical level, I would define a microbeam as a beam which
matches in size with a microcrystal. Then question becomes what is a
microcrystal?
If we wanted to be purely scientific, though, we should not be measuring
anything in mm
21, 2009 3:36 PM
To: Sanishvili, Ruslan
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] How small is a microbeam?
Sanishvili, Ruslan wrote:
.. Reasons for discriminating
5-10 micron beams (minibeam) from ca 1 micron (microbeam) might have
been not so much their size but what it involved
: Nave, C (Colin) [mailto:colin.n...@diamond.ac.uk]
Sent: Tuesday, April 21, 2009 4:44 PM
To: Sanishvili, Ruslan; CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] How small is a microbeam?
Hi
Yes good data with a micron size beam but, in this case, the path length
was 20- 30 micron.
I presume one would
[mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Sanishvili, Ruslan
Sent: Monday, February 23, 2009 12:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Second CCP4 workshop in USA,1st announcement
We are pleased to announce that encouraged by last year's success we are
again organizing CCP4 workshop
bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Sanishvili, Ruslan
Sent: Monday, March 23, 2009 2:04 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CCP4 workshop in the USA, 2nd announcement
This is 2nd announcement of the CCP4 workshop entitled CCP4 school:
From data collection
We are pleased to announce that encouraged by last year's success we are
again organizing CCP4 workshop at Advanced Photon Source (APS), Argonne
National Laboratory (ANL). All details can be found here
http://www.ccp4.ac.uk/schools/APS-2009/
Title CCP4 school: From data collection to structure
Hi Richard and Colin,
There are some X-ray - visible water networks described in 0.66 A
structure of Aldose Reductase (Proteins. 2004 Jun 1;55(4):792-804) and
I'm sure there are plenty of similar descriptions out there.
I am not an expert by any means but I think the question of water
Dear Colleagues,
This is a friendly reminder that the abstract submission deadline for
IUCr Congress in Osaka, Japan is March 31st.
One of the many interesting sessions is entitled Recent progress in
synchrotron data collection (Session number is MS65).
This session will cover new developments
Crystals are supposed to be red if you have oxidized iron in the heme
and deep pink/scarlet if the iron is reduced.
If you removed the iron (for example EDTA during purification) or
substituted with something during purification or crystallization, you
could loose the color.
It is trivial to
Dear Colleagues,
This is second announcement of the CCP4 workshop.
WHAT CCP4 school: From data processing to structure refinement and
beyond.
WHERE Advanced Photon Source, Argonne National Laboratory, near Chicago,
USA.
ORGANIZERS CCP4, University of York, GM/CA-CAT Argonne
PROGRAM
]
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Sanishvili, Ruslan
Sent: Tuesday, January 15, 2008 3:07 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CCP4 workshop in US, 2nd announcement
Dear Colleagues,
This is second announcement of the CCP4 workshop
We are pleased to announce the CCP4 workshop titled
CCP4 school: From data processing to structure refinement and beyond
which will take place on 23-28 of May 2008 at the Advanced Photon Source
(APS) near Chicago.
The aim of this inaugural workshop in the USA will be to cover all areas
My apologies - previous announcement went out with a wrong subject line.
N
We are pleased to announce the CCP4 workshop titled
CCP4 school: From data processing to structure refinement and beyond
which will take place on 23-28 of May 2008 at the Advanced Photon Source
(APS) near Chicago.
Dear colleague,
This is to bring to your attention that there will be a session on Structural
Biology in Neurological Disorders at ACA 2008. Description of the session is
below. We encourage you to submit abstracts for the session and to attend while
at the ACA meeting. Please note that the
Folks,
As expected, discussion about to bathe or not to bathe are starting to
expand into other aspects of data collection and processing. Along the
way I saw reference to how we use our small beams on GM/CA beamlines in
sector 23 of APS. Without going into discussions of advantages and
This may not apply in your case but it is not uncommon for a protein to
precipitate in a microcrystalline shower when put in cold. Once it
worms up, the crystals dissolve and the precipitate clears up. It is
easy to check under a high magnification microscope.
Cheers,
N.
Ruslan Sanishvili
Folks,
Don't take this as an argument with software people - I have a side note about
structures.
Back in the day when I used to solve Structural Genomics structures, we almost
always knew substitution rate from masspec and Se always refined to lesser
occupancy. Could it be the decay instead?
GM/CA-CAT beamlines at APS. Go to
http://www.gmca.anl.gov/userprogram/applying.html
to apply for beamtime.
We provide 5um, 10um, 20um stable beam with fluxes of 1-2x10**11.
Mini-beam (our terminology) has proven itself indispensable for number
of projects covering wide range of crystal
It seems odd from energetic considerations that there would be a
free-form amino acid when it has a choice to be involved in
energetically favorable interaction. It sounds doubly odd in the case of
a cystein involved in a disulfide bond.
Could it be that you are observing the effects of radiation
I am not an expert in XDS but will still put my $0.02 in:
Your new ORGX seems to be a reflection of the 2theta. In some other programs,
origin is always defined at 2theta=0 and the angular (or linear, to that
matter) offset is given as a parameter. I.e. software applies 2theta offset
Hi,
I assume Se-Met is not possible for your protein?
You don't say how well (or poorly) your native crystals diffract.
Increasing number of people are getting their phases by S SAD.
With such affinity to high NaCl concentrations, you could also try high
salt (NaCl, NaBr, RbBr etc,) soaks for
Dear Colleagues,
We are pleased to announce a new mini-beam capability at the two
GM/CA-CAT undulator beamlines in Sector 23 of the APS. We have
implemented an apparatus to produce a strong, stable X-ray mini-beam.
The apparatus is rapidly interchangeable with our standard beam. The
flux and
. Cass Ave.
Argonne, IL 60439
Tel: (630)252-0665
Fax: (630)252-0667
[EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Sanishvili, Ruslan
Sent: Friday, June 15, 2007 9:26 AM
To: CCP4BB
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